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GWASLab-Reference / README.md
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Add dataset card, checksums, EAF, rsID tables, recombination maps, and example sumstats
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metadata 
pretty_name: GWASLab Reference
license: other
license_name: source-data-terms
task_categories:
  - other
tags:
  - gwas
  - genomics
  - 1000-genomes
  - hapmap
  - ld-reference
  - allele-frequency

GWASLab reference datasets

Processed genomic reference files used by GWASLab (download_ref / gwaslab download ref). This dataset replaces the previous Dropbox hosting for GWASLab-processed panels. Official dbSNP VCFs, UCSC FASTA, Ensembl/RefSeq GTF, and liftOver chains stay at their original hosts.

Package catalog: reference.json. Checksums for every file in this repo are in md5sum.txt.

Download with GWASLab 

import gwaslab as gl

gl.download_ref("1kg_eas_hg19")
print(gl.get_path("1kg_eas_hg19"))

gwaslab download ref 1kg_eas_hg19
gwaslab path 1kg_eas_hg19

Direct Hub URL (basename is the local filename download_ref writes):

https://huggingface.co/datasets/Cloufield/gwaslab-reference/resolve/main/1kg/hg19/EAS.ALL.split_norm_af.1kgp3v5.hg19.vcf.gz

Layout

Path GWASLab keyword(s) Use
1kg/hg19/*.vcf.gz (+ .tbi) 1kg_{afr,amr,eas,eur,pan,sas}_hg19 LD / strand / AF (1KGP3v5, hg19)
1kg/hg38/*.vcf.gz (+ .tbi) 1kg_{afr,amr,eas,eur,pan,sas}_hg38 LD / strand / AF (1KG 30x, hg38)
rsid/1kg_dbsnp151_*_auto.txt.gz 1kg_dbsnp151_hg19_auto, 1kg_dbsnp151_hg38_auto SNPID–rsID tables (autosomes)
eaf/PAN.hapmap3.*.EAF.tsv.gz 1kg_hm3_hg19_eaf, 1kg_hm3_hg38_eaf HapMap3 EAF for ancestry
recombination/recombination_hg*.tar.gz recombination_hg19, recombination_hg38 Regional recombination tracks
examples/t2d_bbj.txt.gz (not a catalog keyword) Tutorial BBJ T2D sumstats

Ancestries: AFR, AMR, EAS, EUR, SAS, PAN (all 1KG super-populations combined). Multi-allelic variants were decomposed and normalized; INFO includes population AF.

Processing

1KG VCFs were processed by GWASLab for regional LD plots and strand inference. They are not a substitute for the official 1000 Genomes release files.

Citations

  • GWASLab: He Y, Koido M, Shimmori Y, Kamatani Y. GWASLab: a Python package for processing and visualizing GWAS summary statistics. Jxiv (2023). https://doi.org/10.51094/jxiv.305
  • 1000 Genomes Project: The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature (2015). 30x high-coverage data: Byrska-Bishop et al., Cell (2022).
  • HapMap recombination maps: International HapMap Consortium.
  • BBJ T2D example: Suzuki K et al. Identification of 28 new susceptibility loci for type 2 diabetes in the Japanese population. Nat Genet (2019). Source: http://jenger.riken.jp/

Redistribute and cite the original consortia terms for 1KG, HapMap, dbSNP-derived tables, and BBJ summary statistics.